[phenixbb] Restraining altloc related atoms during refinement

[John Pascal]

>I have my doubts about supporting NCS restraints of alternative
>conformations; the two seem to be mutually exclusive. But maybe
>I don't understand your situtation.

Here are some more details on the refinement situation:
it is possible for a piece of duplex DNA to be positioned in two
conformations in the crystal, and it appears that both conformations
are occupied with roughly the same occupancy.  The sequence is not
completely palindromic, so at some positions a different base is
present depending on the random orientation of the DNA.  However, the
phosphate and ribose atoms occupy the same positions regardless of
the orientation, and I want to enforce this.

>I can see that NCS restraints of backbone atoms only are useful,
>even if the residue names are different.
>The trouble is that atoms in two chains need to be matched
>unambiguously while allowing for chain breaks.
>I could try to simply remove the requirement that the residue names
>have to match and go by residue sequence number + insertion code
>only. Would that work in your case?

Yes, that sounds like it would work.

>A potential downside is that people have to be careful
>excluding non-matching sidechain atoms.

Perhaps it could be that there is an
override option after an error message.

Thanks for your help.

-John

-- 
John Pascal, PhD                       ph 215.503.4596
Assistant Professor                    fx 215.923.2117
Thomas Jefferson University
Biochemistry & Molecular Biology
233 South 10th Street, BLSB 804
Philadelphia, Pennsylvania  19107






----- Forwarded message from John.Pascal at mail.jci.tju.edu -----
    Date: Thu, 20 May 2010 11:54:33 -0400
    From: John Pascal <John.Pascal at mail.jci.tju.edu>
Reply-To: John Pascal <John.Pascal at mail.jci.tju.edu>
 Subject: Restraining altloc related atoms during refinement
      To: phenixbb at phenix-online.org

Hello All,

I would like to restrain the positions of ribose/phosphate atoms of
altloc 'A' to the positions of those in altloc 'B'.  Problem is,
altloc A and altloc B are different residue types, so phenix.refine
exits stating that there are no common atoms when I enter the
following NCS-type restraint:

selection:
chain I and altloc A and resid 1 and (phosphate or ribose)
restrain:
chain I and altloc B and resid 1 and (phosphate or ribose)

I am using the phenix GUI.  Is there a better place to enter this type
of restraint (rather than NCS) that does not care if a P atom is from
a Cd or from a Gd residue type?  thanks.

Best,
John

-- 
John Pascal, PhD                       ph 215.503.4596
Assistant Professor                    fx 215.923.2117
Thomas Jefferson University
Biochemistry & Molecular Biology
233 South 10th Street, BLSB 804
Philadelphia, Pennsylvania  19107






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